Updated on 2021/11/01

写真a

 
YASUDA, Koji
 
Organization
Institute of Materials and Systems for Sustainability Division of Materials Research (DM) Associate professor
Graduate School
Graduate School of Information Science
Graduate School of Informatics
Title
Associate professor
Contact information
メールアドレス

Degree 1

  1. 博士(工学) （ 1997.3   京都大学 ） 

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Research Interests 1

  1. quantum chemistry, many-body theory, density functional theory, reduced density matrices, parallel processing, cheminformatics

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Research Areas 4

  1. Others / Others  / Physical Chemistry

  2. Others / Others  / Mathematical Physics/Fundamental Theory of Physical Properties

  3. Others / Others  / Software

  4. Informatics / Intelligent informatics  / cheminformatics

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Current Research Project and SDGs 4

  1. 化学情報学による物質設計

  2. 表面励起状態の理論化学

  3. グラフィックボードを用いた科学技術計算の加速

  4. Direct determination of the denoity matrix

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Education 2

  1. Kyoto University   Graduate School, Division of Engineering

    - 1997

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    Country： Japan

  2. Kyoto University   Faculty of Engineering

    - 1992

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    Country： Japan

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Professional Memberships 2

  1. 日本物理学会

  2. 日本コンピュータ化学会

    2020.4

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Papers 24

  1. 特徴ベクトルから分子構造を生成するアルゴリズム Invited Reviewed

    陸明浩, 安田耕二

      Vol. 17 ( 5 ) page： 228-231   2019.3

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    Authorship：Lead author   Language：Japanese   Publishing type：Research paper (scientific journal)  

    DOI： 10.2477/jccj.2018-0056

  2. Resonance State Method for Electron Injection in Dye Sensitized Solar Cells

    Sulzer David, Yasuda Koji

    JOURNAL OF CHEMICAL THEORY AND COMPUTATION   Vol. 14 ( 10 ) page： 5090-5104   2018.10

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1021/acs.jctc.8b00364

    Web of Science

  3. A New Method To Evaluate Excited States Lifetimes Based on Green's Function: Application to Dye-Sensitized Solar Cells Reviewed

    David Sulzer, Satoru Iuchi, Koji Yasuda

    J. Chem. Theory Comput.   Vol. 12   page： 3074−3086   2016

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1021/acs.jctc.6b00181

  4. 1. Improving DIIS convergence for metallic systems using Gaussian basis set Reviewed

    David Sulzer, Satoru Iuchi, Koji Yasuda

    Chemical Physics Letters   Vol. 635 ( 16 ) page： 201-204   2015

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  5. Efficient calculation of two-electron integrals for high angular basis functions Reviewed

    Koji Yasuda, Hironori Maruoka

    International Journal of Quantum Chemistry     2013.12

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

    The computation of electron repulsion integrals (ERIs) is the most time-consuming process in the density functional calculation using Gaussian basis set. Many temporal ERIs are calculated, and most are stored on slower storage, such as cache or memory, because of the shortage of registers, which are the fastest storage in a CPU. Moreover, the heavy register usage makes it difficult to launch many concurrent threads on a graphics processing unit (GPU) to hide latency.
    Hence we propose to optimize the calculation order of one-center ERIs to minimize the number of registers used, and to calculate each ERI with three or six cooperating threads. The performance of this method is measured on a recent CPU and a GPU. The proposed approach is found to be efficient for high angular basis functions with a GPU. When combined with a recent GPU, it accelerates the computation almost 4-fold.

    DOI： 10.1002/qua.24607

  6. Acceleration of computatuonal quantum chemistry by Heterogeneous computer architectures Reviewed

    Y. Furukawa, R. Koga, K. Yasuda

    Proceeding of International Conference on Modeling and Simulation Technology     page： 1   2011.10

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    Language：English  

  7. *グラフィックボードで計算物理を Invited Reviewed

    安田　耕二

    日本物理学会誌   Vol. 64 ( 8 ) page： 637-639   2009

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    Authorship：Lead author   Language：Japanese  

  8. *Size extensivity of the variational reduced-density-matrix method Reviewed

    Maho Nakata, Koji Yasuda

    Physical Review A   Vol. 80 ( 4 ) page： 042109   2009

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

    With the density-matrix variational method, the ground-state energy of a many-electron system is calculated by minimizing the energy expectation value subject to the selected representability conditions for the second-order reduced-density matrix (2-RDM). There is a lack of size extensivity under the P, Q, and G conditions of this method by applying to M noninteracting atoms and molecules up to M=32; BeM, (CH4)M, and (N2)M. The energy per molecule (E/M) monotonically decreases as M increases, showing the lack of size extensivity in this method. The inextensive contributions to energies are 3×10-4 and 3×10-3 a.u. for (CH4)M and (N2)M using the STO-6G basis set, respectively. In the examples studied, E/M approaches a finite value as M-->[infinity]. The intermolecular elements of 2-RDMs do not satisfy the cumulant expansion.

  9. Comment on "Family of modified contracted Schroedinger equations" Reviewed

    Koji Yasuda

    Physical Review A   Vol. 79 ( 1 ) page： 016101   2009

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  10. Two-Electron Integral Evaluation on the Graphics Processor Unit Reviewed

    Koji Yasuda

    Journal of Computational Chemistry   Vol. 29 ( 3 ) page： 334-342   2008.2

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  11. *Accelerating Density Functional Calculations with Graphics Processing Unit Reviewed

    Koji Yasuda

    Journal of Chemical Theory and Computation   Vol. 4 ( 8 ) page： 1230-1236   2008

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  12. *The extension of the fragment molecular orbital method with the many-particle Green's function Reviewed

    Koji Yasuda, Daisuke Yamaki

    The Journal of Chemical Physics   Vol. 125   page： 154101   2006.10

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

    By using the many-particle Green's function (GF) the extension of the fragment molecular orbital (FMO) method by Kitaura et al. [Chem. Phys. Lett. 313, 701 (1999)] is proposed. It is shown that the partial summation of the cluster expansion of GF reproduces the same extrapolation formula as that of FMO. Therefore we can determine the excitation energy, the transition moment, and the linear response of a molecule from GF approximated with the FMO procedure. It is also shown that no wave function exists which is consistent to the FMO results. The perturbation expansion in which the self-consistent charge approximation defines the unperturbed state is reported. By using it the three-body effects missing in the pair approximation of FMO are analyzed and the corrections to the energy and the reduced density matrices are proposed. In contrast to the previous works these new corrections are not expressed as the addition or the subtraction of the energies of fragments. They are size extensive and require only the quantities available by the FMO calculation.

  13. Determination of the Hubbard model parameters by using the unrestricted Hartree-Fock solutions, and improvement of their energies Reviewed

    Daisuke Yamaki, Koji Yasuda, Kizashi Yamaguchi

    International Journal of Quantum Chemistry   Vol. 103 ( 1 ) page： 73-81   2005

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    Language：English   Publishing type：Research paper (scientific journal)  

  14. Simple minimum principle to derive a quantum-mechanical/ molecular-mechanical method Reviewed

    Koji Yasuda, Daisuke Yamaki

    Journal of Chemical Physics   Vol. 121   page： 3964   2004

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  15. Uniqueness of the solution of the contracted Schrödinger equation. Reviewed

    Koji Yasuda

    Physical Review A   Vol. 65   page： 052121   2002

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  16. *Local approximation of the correlation energy functional in the density matrix functional theory Reviewed

    Koji Yasuda

    Physical Review Letters   Vol. 88 ( 5 ) page： 053001   2002

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  17. Correlation energy functional in the density matrix functional theory Reviewed

    Koji Yasuda

    Physical Review A   Vol. 63   page： 032517   2001

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  18. Direct determination of second-order density matrix using density equation : Open-shell system and excited state Reviewed

    Nakata M, Ehara M, Yasuda K and Nakatsuji H

    Journal of Chemical Physics   Vol. 112 ( 20 ) page： 8772-8778   2000

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    Language：English   Publishing type：Research paper (scientific journal)  

  19. Direct determination of the guantum-mechanical density matrix : Parquet theory Reviewed

    Physical Review A   Vol. 59 ( 6 ) page： 4133   1999

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  20. Direct determination of density matrix using density equation : potential energy curres of small molecules, HF, CH4, BH3, NH3, and H2O Reviewed

    Ehara M, Nakata M, Kou H, Yasuda K and Nakatsuji H

    Chemical Physics Letters   Vol. 305 ( 5-6 ) page： 483-488   1999

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    Language：English   Publishing type：Research paper (scientific journal)  

  21. Direct determination of the quantum-mechanical density matrix using the density equation II. (共著) Reviewed

    Physical Review A   Vol. 56 ( 4 ) page： 2648   1997

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  22. Direct determination of the quantum-mechanical denoity Matrix using the density equation(共著) Reviewed

    Physical Review Letters   Vol. 76   page： 1039   1996

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  23. Theoretical Study of the Vacuum-Ultraviolet Spectra of SnH4 and Sn(CH3)4(共著) Reviewed

    The Journal of Physical Chemiotry   Vol. 99   page： 12501   1995

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

  24. Theoretical Study of the Visible and Ultraviolet Spectra of Chromyl Chloride(CrO2Cl2)(共著) Reviewed

    The Journal of Chemical Physics   Vol. 99   page： 1945   1993

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

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Books 1

  1. 分子システムの計算科学

    安田耕二, 天能精一郎, 他（ Role： Joint author）

    共立出版  2010.11 

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    Language：Japanese

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Presentations 30

  1. 特徴ベクトルから分子構造を生成するアルゴリズム

    陸明浩, 安田耕二

    日本コンピュータ化学会2018秋季年会  

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    Event date： 2018.11

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：弘前大学   Country：Japan  

  2. Green関数を用いた表面励起状態の計算法

    Sulzer David, 井内哲, 安田耕二

    分子科学討論会2016 

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    Event date： 2016.9

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：神戸ファッションマート   Country：Japan  

  3. Theoretical Analysis of the Electron Injection Rate in the Dye-Sensitized Solar Cells International conference

    David Sulzer, Satoru Iuchi, Koji Yasuda

    International Symposium on EcoTopia Science 2015 (2015). 

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    Event date： 2015.11

    Language：English   Presentation type：Poster presentation  

    Country：Japan  

  4. Theoretical Analysis of the Electron Injection Rate in the Dye-Sensitized Solar Cells International conference

    David Sulzer, Satoru Iuchi, Koji Yasuda

    The 6th JCS (Japan-Czech-Slovakia) Symposium on Theoretical Chemistry 

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    Event date： 2015.10

    Language：English   Presentation type：Oral presentation (invited, special)  

    Country：Slovakia  

  5. Toward Improvement of DSSC through Calculation of Lifetime International conference

    David Sulzer, Satoru Iuchi, Koji Yasuda

    The satellite symposium of International Congress of Quantum Chemistry 2015: Novel computational methods for quantitative electronic structure calculations 

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    Event date： 2015.6

    Language：English   Presentation type：Poster presentation  

    Country：Japan  

  6. Theoretical study of the structure and property of Pt nanoparticles in solution International conference

    Koji Yasuda

    International Symposium on EcoTopia Science 2013 

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    Event date： 2013.12

    Language：English   Presentation type：Oral presentation (general)  

    Country：Japan  

  7. Quantum Chemistry on GPUs

    Koji Yasuda, Ryota Koga

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    Event date： 2013.6

    Language：Japanese   Presentation type：Oral presentation (invited, special)  

    Country：Japan  

  8. Acceleration of Quantum Chemistry and Chemical Similarity calculations on GPGPU architecture towards faster virtual screening International conference

    R. Koga, Y. Furukawa, K. Yasuda

    245th ACS National Meeting 

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    Event date： 2013.4

    Language：English   Presentation type：Poster presentation  

    Country：United States  

  9. メニーコアプロセッサと量子化学

    安田耕二

    第3回CMSI研究会 

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    Event date： 2012.12

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：自然科学研究機構　岡崎コンファレンスセンター   Country：Japan  

  10. Acceleration of Quantum Chemistry and Chemical Similarity calculations on GPGPU architecture towards faster virtual screening

    Y. Furukawa, R. Koga, K. Yasuda, N. Nariai

    Joint Conference on Informatics in Biology, Medicine and Pharmacology 

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    Event date： 2012.10

    Language：English   Presentation type：Poster presentation  

    Country：Japan  

    The possibility of the molecular modeling and the virtual screening increases as the increase of the computational resources. Today biologically important macromolecules, such as proteins, are within the scope of electronic-structure calculation by using fragment molecular orbital (FMO) method. Also there are several well established methods to measure chemical similarity computationally. LINGO is such a method by comparing SMILES representations of two molecules. Looking at the development of recent computer, many-core processors such as graphics processing units (GPUs) would be key technology for future high-performance computation. General-purpose GPU (GPGPU) is successfully applied for many kinds of problems in high performance computation.
    Since 2007 we developed the method to accelerate the molecular orbital calculation by using NVIDIA GPUs. This study produced the XA-CUDA-QM add-in library to accelerate standard QM software (GAMESS-US etc). Recently we extended its functionality such as using d-orbital basis set, FMO trimer calculation (FMO3), and energy gradient calculation, which will be presented. We also examine a performance on the newest NVIDIA's GPU, GTX680, called Kepler, and found it excellent to accelerate FMO.
    Second, we develop a LINGO similarity calculation method to utilize both CPUs and GPUs at the same time. Our method is based on SIML reported to accelerate LINGO by using GPGPU.

  11. メニーコアプロセッサによる量子化学とその応用

    安田 耕二，古川 祐貴，古賀 良太

    分子科学討論会2012 

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    Event date： 2012.9

    Language：Japanese   Presentation type：Poster presentation  

    Venue：東京大学　本郷キャンパス   Country：Japan  

  12. Acceleration of computational quantum chemistry by AVX + CUDA on heterogeneous computer architectures International conference

    Yuki Furukawa, Ryota, Koji Yasuda

    242th ACS National Meeting & Exposition 

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    Event date： 2012.3

    Language：English   Presentation type：Poster presentation  

    Country：Japan  

  13. Accerelation of Quantum Chemistry and Chemical Similarity calculations on GPGPU architecture toward faster virtual screening International conference

    Y. Furukawa, R. Koga, N. Nariai, K. Yasuda

    [2] International Conference on Rare Diseases & Orphan Drugs 2012 

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    Event date： 2012.2

    Language：English   Presentation type：Oral presentation (general)  

    Country：Japan  

  14. Rational Material Design by Quantum Chemistry International conference

    Koji Yasuda, Yuji Kawamatsu

    International Symposium on EcoTopia Science 

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    Event date： 2011.12

    Language：English   Presentation type：Poster presentation  

    Country：Japan  

  15. メニーコアプロセッサによる量子シミュレーション

    安田耕二

    第34回情報科学討論会 

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    Event date： 2011.11

    Language：Japanese   Presentation type：Oral presentation (keynote)  

    Venue：長崎大学文教キャンパス   Country：Japan  

  16. Acceleration of computational quantum chemistry by heterogeneous computer architectures International conference

    Y. Furukawa, R. Koga, K. Yasuda

    [1] JSST 2011 International Conference on Modeling and Simulation Technology 

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    Event date： 2011.10

    Language：English   Presentation type：Oral presentation (general)  

    Country：Japan  

  17. 並列対角化による密度行列の解法

    川松裕史, 安田耕二

    第５回分子科学討論会 

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    Event date： 2011.9

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：札幌コンベンションセンター   Country：Japan  

  18. Parallel Diagonalization and the Density Matrix International conference

    Koji Yasuda

    JCS Symposium on Theoretical Chemistry 2011 

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    Event date： 2011.5

    Language：English   Presentation type：Oral presentation (general)  

    Country：Czech Republic  

  19. Parallel diagonalization and the density matrix completion International conference

    Yuji Kawamatsu, Koji Yasuda

    The 4th Japan-Czech-Slovak (JCS) Symposium for Theoretical and Computational Chemistry 

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    Event date： 2011.5

    Language：English   Presentation type：Poster presentation  

    Country：Czech Republic  

  20. Acceleration of FMO by CPU-GPGPU hybrid calculation International conference

    Yuki Furukawa, Ryota Koga, Koji Yasuda

    241st ACS National Meeting & Exposition 

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    Event date： 2011.3

    Language：English   Presentation type：Poster presentation  

    Country：Japan  

  21. Acceleration of fragment molecular orbital method by GPU International conference

    SC10 

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    Event date： 2010.11

    Language：English   Presentation type：Poster presentation  

  22. メニーコアプロセッサによる量子化学計算

    CMSI研究会「新量子相・新物質の基礎科学」 

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    Event date： 2010.11

    Language：Japanese   Presentation type：Oral presentation (general)  

    Country：Japan  

  23. GPUを用いたフラグメント分子軌道法の高速化

    古賀良太、古川祐貴、安田耕二

    CBI学会2010年大会 

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    Event date： 2010.9

    Language：Japanese   Presentation type：Oral presentation (general)  

    Country：Japan  

  24. GPGPUによる量子化学計算の高速化

    古川祐貴、古賀良太、安田耕二

    分子科学討論会2010 

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    Event date： 2010.9

    Language：Japanese   Presentation type：Poster presentation  

    Country：Japan  

  25. 量子化学計算について

    安田耕二

    第２回アクセラレーション技術発表討論会 

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    Event date： 2010.9

    Language：Japanese   Presentation type：Oral presentation (general)  

    Country：Japan  

  26. GPGPUは電子状態計算に使えるか

    安田耕二

    第23期CAMMフォーラム7月合宿例会本例会 

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    Event date： 2010.7

    Language：Japanese   Presentation type：Oral presentation (invited, special)  

  27. Harvard-Riken Joint Symposium :Application of GPU Computation to Brain Science, Quantum Science, Astronomy, Fluid Dynamics and other sciences

    Density Functional Calculations on GPUs 

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    Event date： 2009.8

    Language：English   Presentation type：Poster presentation  

    Country：Japan  

  28. ストリーミングプロセッサによる科学技術計算

    シンポジウム「革新的量子化学の展開」 

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    Event date： 2009.5

    Language：Japanese   Presentation type：Oral presentation (invited, special)  

    Country：Japan  

  29. Local approximation of the correlation energy functional in the density matrix functional theory International conference

    安田耕二

    WE-Heraeus-Seminar: Modern Aspects of Many-Electron Theory 

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    Event date： 2001

    Language：English   Presentation type：Poster presentation  

  30. Electronic structure theory based on the reduced density matrices

    安田耕二

    Okazaki Conference “Molecular Orbital Theory for the New Millennium” 

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    Event date： 2000

    Language：English   Presentation type：Oral presentation (invited, special)  

    Country：Japan  

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Other research activities 1

  1. Comment on Energy-Time Uncertainty Relations in Quantum Measurements

    2018.9

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    arXiv.org > quant-ph > arXiv:1809.06539

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Research Project for Joint Research, Competitive Funding, etc. 4

  1. フラグメント分子軌道法を中核とした量子計算創薬システムの開発

    2011.4 - 2012.3

    科学技術振興機構 A-STEP フィージビリティスタディ（シーズ顕在化タイプ、起 業検証タイプ） 

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    Grant type：Competitive

  2. GPGPUによる量子化学計算の高速化

    2010.4 - 2010.9

    国内共同研究 

  3. GPGPUによる量子化学計算の高速化

    2009.10 - 2010.3

    国内共同研究 

  4. ＧＲＡＰＥ型専用計算機による量子化学

    2006

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KAKENHI (Grants-in-Aid for Scientific Research) 6

  1. Precise Molecular Design of Organic Friction Modifiers by Large-Scale Molecular Simulations, Advanced Measurements, and Chemical Syntheses

    Grant number：21H01238  2021.4 - 2024.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

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    Authorship：Coinvestigator(s) 

  2. グラフニューラルネットワークによる有機遷移金属反応の機械学習

    Grant number：21K12027  2021.4 - 2024.3

    科学研究費助成事業  基盤研究(C)

    安田 耕二

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    Authorship：Principal investigator 

    Grant amount：\2990000 （ Direct Cost: \2300000 、 Indirect Cost：\690000 ）

    この研究は、既知の有機遷移金属反応を特別なニューラルネットに学習させて、新規反応をひらめかせたり、良い遷移金属触媒を発見することを目指します。そのために、遷移金属を含む分子構造をはっきり認識する、グラフニューラルネットを開発します。また、有機遷移金属の反応を実験論文などから収集し、データベースを構築します。ニューラルネットに反応パターンを学習させ、新しい反応を予想します。これを量子化学計算でシュレーディンガー方程式を解き検証します。人工知能でこの手続きを自律的、大規模かつ徹底的に行い、実験化学者の知能を超える事を目指します。

  3. 太陽電池における光電変換の基礎過程の研究と変換効率最適化・長寿命化にむけた大規模数値計算

    2014.4 - 2015.3

    科学研究費補助金  「HPCI戦略プログラム」分野2（新物質・エネルギー創成）第四部会 特別支援課題

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    Authorship：Principal investigator 

  4. GRAPE型専用計算機による量子化学

    2006.4 - 2008.3

    科学研究費補助金  若手研究(B)

    安田耕二

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    Authorship：Principal investigator 

  5. 完全基底関数効果を含む分子軌道法の開発と応用

    2001.4 - 2004.3

    科学研究費補助金  基盤研究(B)

    天能 精一郎

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    Authorship：Coinvestigator(s) 

  6. 分子や固体の電子状態を解明する、密度行列汎関数理論の開発

    1999.4 - 2002.3

    科学研究費補助金  特定領域研究

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    Authorship：Principal investigator 

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To the head of KAKENHI (Grants-in-Aid for Scientific Research).▲
 

Teaching Experience (On-campus) 19

  1. 化学情報学特論

    2018

  2. 大規模複雑系計算特論

    2018

  3. 化学基礎II

    2018

  4. 大規模複雑系計算特論

    2017

  5. 情報可視化論特論

    2017

  6. 化学情報学特論

    2017

  7. 化学基礎II

    2017

  8. 化学基礎II

    2016

  9. 対称性と微分方程式特論

    2015

  10. 化学基礎II

    2015

  11. 化学基礎II

    2014

  12. 複雑系科学特論

    2014

  13. 化学基礎II

    2013

  14. 対称性と微分方程式特論

    2013

  15. Fundamentals of Chemistry II

    2012

  16. Fundamentals of Chemistry II

    2011

  17. 複雑系科学特論

    2011

  18. 化学基礎II

    2009

    　詳細を見る

    物理化学、量子化学の入門を講義する。

  19. 複雑系科学実験1

    2009

    　詳細を見る

    数値計算、古典力学の計算機シミュレーション、並列処理について講義し、実習を行う。

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